[gmx-users] autocorrelation function of hydrogen bond : g_hbond

[Nilesh Dhumal]

Is oscillation is because of change in hydrogen bonded distance?

Do program consider the change in hydrogen bonded distance during ACF
calculation?

Nilesh

> There's a known oscillation in the ACF that occurs at ~100 fs or so. Is
> that what you see?
>
> Erik
>
> On 9 Apr 2013, at 18:02, Nilesh Dhumal <ndhumal at andrew.cmu.edu> wrote:
>
>>
>>
>>> On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal
>>> <ndhumal at andrew.cmu.edu>wrote:
>>>
>>>> Hello,
>>>>
>>>> I am calculating the hydrogen bond autocorrelation function using
>>>> g_hbond
>>>> for O-H---O hydrogen bond in system.
>>>>
>>>> I made two groups 1. O-H atoms numbers 2. two oxygen atoms are
>>>> interacting
>>>> with OH bond.
>>>>
>>>> I am using default hydrogen bond criteria (donor-acceptor distance 3.5
>>>> and
>>>> angle 30) for calculating the autocorrelation function.
>>>>
>>>> I am not getting a smooth exponential plot. I get a small bump in the
>>>> plot.
>>>>
>>>> Attached the autocorrelation plot.
>>>>
>>>>
>>> Attachments are not allowed on this list. Please provide a link to the
>>> image.
>>>
>>>
>>>> Why there is not smooth exponential plot.
>>>>
>>>
>>> There is no way to tell, and even with the image there is still no way
>>> to
>>> tell. How much sampling do you have? Have you looked at overall
>>> convergence, etc?
>>
>>
>> I saved the trajectory at 3fs.
>>
>> It converged.
>>
>> Nilesh
>>
>>
>>
>>
>>>
>>> -Justin
>>>
>>> --
>>>
>>> ========================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540)
>>> 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
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